You can uninstall the unmanaged SEP then deploy SEP from SEPM or you can import the communication setting file to the unmanaged SEP.

Export sylink.xml from SEPM and import sylink.xml to SEP
You can export communication settings from Default group or you may wish to create your own group and export the communication setting from your created group.

You may wish to export your sylink.xml file to your thumb drive or share folder.